[2026-06-08T08:20:40] Launching Arriba 2.4.0
[2026-06-08T08:20:40] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:20:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:20:52] Reading chimeric alignments from 'GM24385_0001_RNA_0001_23H5VFLT4_s16.Aligned.sortedByCoord.out.bam' (total=13468665)
[2026-06-08T08:27:55] Marking multi-mapping alignments (marked=9838080)
[2026-06-08T08:28:00] Detecting strandedness (reverse)
[2026-06-08T08:28:00] Assigning strands to alignments 
[2026-06-08T08:28:03] Annotating alignments 
[2026-06-08T08:28:51] Filtering duplicates (remaining=6637186)
[2026-06-08T08:29:00] Filtering mates which do not map to interesting contigs (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*) (remaining=5754617)
[2026-06-08T08:29:03] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5754617)
[2026-06-08T08:29:05] Filtering viral contigs with expression lower than the top 5 (remaining=5754617)
[2026-06-08T08:29:11] Filtering viral contigs with less than 5% coverage (remaining=5754617)
[2026-06-08T08:29:14] Estimating fragment length (mate gap mean=-83.211, mate gap stddev=30.6929, read length mean=124.309)
[2026-06-08T08:29:14] Filtering read-through fragments with a distance <=10000bp (remaining=5513456)
[2026-06-08T08:29:17] Filtering inconsistently clipped mates (remaining=5400899)
[2026-06-08T08:29:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4721735)
[2026-06-08T08:29:26] Filtering fragments with small insert size (remaining=4720234)
[2026-06-08T08:29:28] Filtering alignments with long gaps (remaining=4720234)
[2026-06-08T08:29:31] Filtering fragments with both mates in the same gene (remaining=4718425)
[2026-06-08T08:29:33] Filtering fusions arising from hairpin structures (remaining=4362964)
[2026-06-08T08:29:36] Filtering reads with a mismatch p-value <=0.01 (remaining=1695035)
[2026-06-08T08:29:48] Filtering reads with low entropy (k-mer content >=60%) (remaining=937991)
[2026-06-08T08:29:58] Finding fusions and counting supporting reads (total=840633)
[2026-06-08T08:30:18] Merging adjacent fusion breakpoints (remaining=833701)
[2026-06-08T08:30:20] Filtering multi-mapping fusions by alignment score and read support (remaining=403433)
[2026-06-08T08:31:02] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:31:10] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=400225)
[2026-06-08T08:31:11] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=286705)
[2026-06-08T08:31:12] Filtering fusions with <2 supporting reads (remaining=18964)
[2026-06-08T08:31:13] Filtering fusions with an e-value >=0.3 (remaining=3989)
[2026-06-08T08:31:14] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4021)
[2026-06-08T08:31:18] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3545)
[2026-06-08T08:31:19] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3545)
[2026-06-08T08:31:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3368)
[2026-06-08T08:31:27] Searching for fusions with spliced split reads (remaining=3437)
[2026-06-08T08:31:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=2420)
[2026-06-08T08:31:35] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2390)
[2026-06-08T08:31:36] Searching for fusions with >=4 spliced events (remaining=2807)
[2026-06-08T08:31:38] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=995)
[2026-06-08T08:31:51] Filtering fusions with anchors <=23nt (remaining=760)
[2026-06-08T08:31:52] Filtering end-to-end fusions with low support (remaining=733)
[2026-06-08T08:31:53] Filtering fusions with no coverage around the breakpoints (remaining=725)
[2026-06-08T08:31:54] Indexing gene sequences 
[2026-06-08T08:31:58] Filtering genes with >=30% identity (remaining=205)
[2026-06-08T08:31:59] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=60)
[2026-06-08T08:32:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=57)
[2026-06-08T08:32:03] Searching for additional isoforms (remaining=79)
[2026-06-08T08:32:05] Assigning confidence scores to events 
[2026-06-08T08:32:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:32:09] Writing fusions to file 'GM24385_0001_RNA_0001_23H5VFLT4_s16.arriba.fusions.tsv' 
[2026-06-08T08:32:10] Writing discarded fusions to file 'GM24385_0001_RNA_0001_23H5VFLT4_s16.arriba.fusions.discarded.tsv'
[2026-06-08T08:32:41] Freeing resources
[2026-06-08T08:33:04] Done (elapsed time=00:12:24, CPU time=00:12:23, peak memory=18.7gb)